Computer method, apparatus and system for merging software configurations. The invention system and method includes a workspace providing a work environment in which to perform operations on a subject software configuration. The workspace identifies a change set of current changes being made to the subject software configuration. A merge tool is coupled to perform software configuration merges in the workspace. The workspace accumulates change sets in a merge of each artifact forming the subject software configuration and passes the accumulated change sets to the merge tool. Consequently, artifact merges are made in the context of substantially all previous merge decisions. The workspace also tracks deferred change sets and the system enables a user to re-invoke the merge tool with respect to artifacts having deferred change sets.